A tentative schedule of things we will do over the first few weeks. Link to the old Daily Schedule Summ13 Researcher's Names: VDSers: Andrei, Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki Sidestreamers: Hailey, Zain HSers: Sarah, Minsu, Braxton, Roshni, Caroline W. Lab Safety: Have you complete your lab safety trainings? Schedules: please enter your summer schedule here (e.g. classes that you may be taking in the summer or other conflicts with lab work): LINK HERE Mentors: Want to know when the mentors will be on? - check here Google Calendar Mentor Conflict sheet
NOTE - see very bottom of page for previous weeks' schedules and things to catch up on that you may have missed.
Mentor Tasks:
make competent cells using Joey's protocol - HSers doing
make PFU polymerase - HSers doing
Set up Mendeley account for VDS. - DONE
Mentor
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Enzyme assay on YopH or FtHap (whichever one you made)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
MENTOR:
Tally hours from last week and enter into spreadsheet on VDSStaff
RESEARCHERS
Update Wikipages - Brianna, Andee, Luis, Martin, Braxton
Update notebooks:
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
Info from your Target Page (which means you need a Target page first!)
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
Print Journal Club article for you and your friends
Make LB for next week (500ml per person)
Agarose gel checks
Lab Notebook check - should have everything up to date.
-- sleep all day
-- watch TV all day
Dr. B NOTES:
Middle Schoolers visit lab
Mentors: prepare RE digest products for MSers
Cool Stuff We May Not Get To:
Library generation and ligand prep for virtual
Homology modelling
Screening with ICM
Staff Stuff:
Label new reagents and supplies
Dilute new 100 bp ladder in Blue Juice + TE
Target Discovery choices --> order primer sets
ToDo List:
Lab Notebook Checks
Protocol cost analysis (Transformation, cloning)
Walk through |protein expression (use current mentor's enzymes)
Joey & Christina's Francisella HAP enzyme
Sadhana's M. tuberculosis enzyme
Joshua's M. tuberculosis enzyme
J.C.'s YopH
Wednesday, July 30, 2014 Thursday, July 31, 2014 Friday, August 1, 2014
Mentors
Edit SignInSheetCLASS_VDSLabSummer14.xlsx and print several (and hand write date on there)
Update Autoclave and Big Centrifuge Protocols and put in binder. Attach Big Centrifuge protocol to Big Centrifuge.
Print 'Sign-Off' sheets for the Biq Equipment usage (See One, Do One, Teach One) -- GDocs/Misc/
--- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Blue.docx - DONE
--- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Pink.docx - DONE
make Research Pages Summer (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student - DONE Melissa
make Journal Club page for Summer 2014 (see previous journal club for 2013 summer and modify) - DONE Dr. B
Week 1
Post your [[#|class schedule]] to GDOcs - Summer14 - ?
Create your own folder in Google Docs under the folder: /StudentFolders
Thursday, June 5
First meeting 3:30 PM - PAI 2.14 (the wet lab)
-- then we will walk over to GEA 100
Lab Safety training
- New guys - walk through with Dr. B
sign up for FF205 (firefighter training) Lab Safety classes
New guys - have lots of [[#|online classes]] to take too - see the link above
Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
Those that don't have to do Safety Training Walk Through with Dr. B
Pick up primers in MBB with mentors
Dilute some primers
ProtocolPrimerDilutionVDS_Summ14.docx
M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2
label very well, place in primers box
Friday, June 6
1:00 PM start time.......meet in PAI 2.14 to start
Pick up primers at MBB (as a group) - if not already done.
Target Discovery in computer lab WEL 2.128
Saturday, June 7 - watch TV Sunday, June 8- watch TV
Week 2
Monday, June 9 @ 1pm - Computer lab - Target Disco con't..... later in afternoon:
Tuesday, June 10
Create your own folder in Google Docs under the folder: /StudentFolders
Make LB (definitely Zain + partner and Hailey + partner) and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans)
LB = 4 x 500 ml amounts
LB plates (20ml per plates) --> make 10 AMP plates (divide into 2 groups) + 36 KAN plates (divide into 3 groups)
to Autoclave
while autoclave go to Nanodrop & submit to DNA sequencing.
Determine concentration of a plasmid (even if it already has it written on the tube!)
(- you pick: pGBR22 or pGFP or pmCherry)
Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc
'Learn how to submit to DNA sequencing' (starring Grace et al.) - wet lab
ProtocolDNASequencingFacilityVDS_Summ14.doc
submit pGBR22, pGFP, or pmCherry using forward or reverse primer - but not both
post results into the RESULTS folder of GDocs
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
Lab Group Meeting @ 5:30 - 6:30 pm
GEA 403
1st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496. Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Wednesday, June 11
Those that don't have to do Safety Training Walk Through with Dr. B
SIgn up for a DNA sequenging [[#|account]] on DNA Lims.
ProtocolDNASequencingFacilityVDS_Summ14.doc
post results into the RESULTS folder of GDocs
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)
Lab clean up
- surfaces, fridges, old plates, old reagents, glassware
re-hang PDB Drug Poster
hang 2014 VDS Stream poster
Organize powdered chemicals
Clean Stir bars
Fill & label spray bottles
Write items needed on whiteboard
Prep collirollers
clean glassware (from Kaarthik)
SHOPPING! ---
go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring several styrofoam containters)
Get stuff from -80degC in Biotech and Robertus Labs (competent cells, protein, etc)
-- store in our -80degC in racks
Proper freezer box label orientation
visit storerooms (walking by ICMB storeroom, then to biotech lab),
purchase the following items (see purchasing spreadsheet in GDocs /Misc/Purchasing) - PRINT IT OUT for 3 teams
- sharpies, spray bottles
- Taq DNA polymerase, 100bp and 1kb ladders
- Mini prep kit, midi prep kit, PCR cleanup kit, IPTG, DTT, TCEP
Enter purchase information in spreadsheet
Place receipt in Dr. B's 'receipt' cubby
prep new kits (midi, mini, PCR cleanup kits)
Analyze DNA Sequence Exercise as a group - ?
Thursday, June 12
Analyze DNA Sequence Exercise as a group -NO
Those that don't have to do Safety Training Walk Through with Dr. B
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry or pNIC-Bsa4 or pUC19)
Several people: Transform a plasmid for Midi-prep
Some transform expression plasmids (BL21(DE3)) - IF DOING ONE OF THESE _ ALTER THE PROTOCOL TO not USE DH5alphas
Grow up colonies of PFU polymerase for eventual midi-prepping. - Melissa
- start 2x 5ml LB overnight culture of Pfu colonies in Kanamycin (use exiisting plate)
- start 2x 5ml of glycerol stocks overnight culture in Kan
- spread 2 x glycerol stocks onto Kan plates.
-- let me know if they grow.
--- then later date proceed to large scale culture
Friday, June 13
check plates - image and upload results to Wikispaces Resarch page and to your Google Docs folder, paste into your lab notebook
- store plates by wrapping in parafilm (just the perimeter) and storing upside down in 4degC in blue racks
check DNA sequenging results - put on Wiki and in notebook
Clean out fridge by the front of the lab (has a bunch of old LB)
Biohazard Waste Boxing Demonstration
Make more LB+Kan plates, make more LB media for next weeks expressions
Mentor
- make notes about Pfu polymerase in the MentorLabLog - in GDrive
- check Pfu polymerase colony growth from yesterday (from melissa and Grace)
-- if it grew - spread a little bit out on a new Kan plate.
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page
Target Discovery selections
Protocol Primer Design OverlapAssembly
Order Overlap Primers for class
On Your Targets Page:
Add Link to DNA Works output text file
Add substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
Saturday, June 14 Sunday, June 15
WEEK3 Monday, June 16, 2014
Wikispaces:
Update Wikispaces Page: Andee, Andrei, Carolyn, Zain
Just add DNA sequencing result to Wikispaces: Brianna, Charina, Chris, Cidia,Hailey
Completed Wikispaces: Luis, Nicole
Mentor - print new VDS SIgn IN sheets, write dates on them and put in binder (it is in the Google Docs for VDSclass/Scheduling)
Dr. B out 1-3pm, 4-5 pm
Make more LB+Kan plates (10), LB+Kan+Sucrose (20), LB+Amp (10), make more LB media for expressions (2 liters worth, best if they are in separate Erlenmeyer flasks that they will be doing the expessions in)
--e.g. for a 80 ml expression - put it ina 500ml flask
--.e.g for a160 ml expression - put it in a 1000 ml Erlenmeyer flask
-- rule of thumb is that volume of container is 4-5 times bigger than volume of media.
While the autoclave is running, Make some 20% sucrose.
Fill water bath shakers with water and get to temp
[[#|Install]] flask clamps.
Someone do a single transformation of FtHap into BL21(DE3) - just one plate - not the 3 plate thing.
Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware
Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)
Transformation Efficiency calculations.
Mentor - grow up a colony of PFU Polymerase from DR. McDonald overnight.
Mentor - make Research Pages Summer for the new High School students (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student -
Grow up DH5alpha cells for Plasmid Preps:
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.
-- for each plasmid in DH5alpha, see the MidiPrep protocol
HIGH COPY PLASMIDS:
w/ Amp in 2x80 ml of LB: (80ml is one 'culture's worth. The other 80 ml is a backup)
pGBR22 - Andrei
pGFP - Andee
pmCherry - Briana
LOW COPY PLASMIDS:
w/ Kan in 1x160ml of LB: (160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator)
pNIC-Bsa4 - Carolyn, Hailey, Chris T and Nikki
pNIC-Bsa4 - Charina, Zain, Cidia, Luis
NOTE: the Kan or Amp is not what makes them high or low copy. It is a function of the plasmid. You get more copies of DNA made from a high copy plasmid.
Follow this protocol for the following plasmids: pGBR22, pGFP, pmCherry
ProtocolTransformationforPlasmidPrepVDS.doc
Follow this protocol for the following plasmids: pNic-Bsa4
ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v4
ToDo: next day (Tuesday) spin down your samples. We need to do this in the mid-morning. So, I would like one person to come in around 10:30 and move everyone's Erlenmeyer flasks to the 4degC fridge to 'stop' their growth until the rest of us can get there at 1:00 pm.
5:00-5:30 - Chris T and Carolyn T and Dr. B meet to discuss paper and slides.
Tuesday, June 17, 2014
10:30 - one unlucky person gets to come in and move the flasks to the 4degC fridge. - Nicole W. (mentor)
1:00 PM - spin down your cultures from yesterday. [[#|Store]] pellets in -20degC.
Charina - check FtHap plates
Make some more LB (3 liters)
Make some 20% sucrose.
Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware
Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)
High Schoolers 1st day
- get setup on GDrive, Wikispaces, etc - pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS) - PyMol 1 lab Eventually, someone transform FtHap into BL21(DE3) & DH5alphas
- and transform YopH into DH5alphas
Make 3L LB - Cidia, Luis, Charina
Make 20% Sucrose - Zain, Nikki
My First PCR - Cidia, Luis, Charina, Zain, and Nikki
MidiPrep-
pGBR22 - Andrei and Carolyn
pFGP - Andee, Hailey, Briana
Overnight Cultures for [[#|Protein Expression]]:
YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris
FtHap - Luis & Andrei, Charina & Nikki
Dilute some primers (go in this order until we run out of new primers to dilute) - Andrei, Hailey, Zain HSers: Sarah, Minsu, Braxton, Roshni, Caroline W.
Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
ProtocolPrimerDilutionVDS_Summ14.docx
M13f, M13r, SP6, T7, VDS1, VDS2, VDSR1, VDSR2
label very well, place in primers box for VDS
Lab Group Meeting @ 5:30 - 6:30 pm
GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, June 18, 2014
Protein Expression - all day - this means that we have to start in the morning (10:00)
HSers - Buffers & Solutions lab
Make IPTG - sterile filter
---- 1 M IPTG in nanopure
Make Lysis buffer (see purification protocol)
LYSIS BUFFER (for sonication)
Tris
50
mM
NaCl
300
mM
Imidazole
10
mM
pH 8.0 w/ NaOH
submit Midiprep plasmids to DNA sequencing (for those that did Midiprep)
[[#|start]] agarose gels of 1st PCR ?
Luis & Cydia & Nikki
-- start an overnight culture of pNIC-Bsa4 in DH5alpha for making more DNA plasmid for MidiPrep
----2 x 160ml of LB + Kan
-- steal from the plates of: Carolyn, Hailey, Charina, or Zain
-- spin down tomorrow
Thursday, June 19, 2014
HSers - Nanodrop and submit to DNA sequencing pGBR22
Luis, Cydia, Nikki - spin down overnight cultures of DH5alphas
Protein Expression Groups:
YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris
FtHap - Luis & Andrei, Charina & Nikki
Sonication - and store in -20degC
-- These guys start first:
MidiPrep (for those that haven't done it yet) - Zain, Cidia, Chris, Luis, Charina, Nikki
-Use this Kit Protocol for each one.
-ProtocolMidiPrepKit_HiSpeed_VDS_v3.doc
Agarose gels for those that have done PCR.
My first PCR
Nickel purify samples from sonication. Collect samples for characterization gel. Store main elution samples in 4degC for next week
start agarose gels of 1st PCR
Restriction Enzyme digest
My First PCR - for those that haven't done it yet
Mentor - grow up overnight culture of pBGR22 in DH5alpha for midi-prep
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES
Put a line and 'Week3' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder
PCR pLIC
Safety training check.
distribute collirollers to tubes (sterily)
Mentor - check lab notebooks to see if up to date.
Monday, June 23, 2014
re-do 1st PCR if failed
- if it works, proceed to PCR pLIC
Analyze DNA Sequence as group
HSers - make more LB,
grow up pGBR22 colonies overnight in 2x80ml of LB each
Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder
Tuesday, June 24, 2014
Input information about which culture of plasmid you have (or will) grow up. GoogleDocs/Misc/Plasmid Concentrations https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Nickel Purification, Characterization,
practice PCRs
Midi-prep pGBR22 (high schoolers) *Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, June 25, 2014
HSers: make LB, make plates, submit DNA to sequencing that you made yesterday
Expression and Spin down for those re-doing protein expression
work on PCRs
Protein Gel for - Andrei, Luis, Andee, Carolyn (maybe do FPLC too?)
Thursday, June 26, 2014
Take ownership of the Target Page for your new target on Wikispaces (update, revise or create page) http://vdsstream.wikispaces.com/Targets
Lab Tour - there is a lab tour today by visitors - so it is doubly important to wear proper clothing in lab (long pants and close toed shoes)
Purification & Protein gels for people who expressed protein yesterday
FPLC, storage - Andrei, Luis, Andee, Carolyn
Make Oligo mix for Targets
PCR pLIC (2nd practice PCR)
Design Tail Primers for targets, order tail primers
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES
Put a line and 'Week4' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, June 28, 2014 Sunday, June 29, 2014
WEEK 5
Monday, June 30, 2014
Wikispaces to be updated: Andee, Andrei, Carolyn, Sarah, Martin, Braxton, Caroline, Roshni
Figure out FPLC schedule - who has YopH, vs FtHap. Who can do Wed 11am.
Make Oligo mix for Targets
PCR pLIC (2nd practice PCR)
Make FPLC buffers
print journal club article (and read) for tomorrow - it's a long one!
High schoolers do RE Digest
Week 5
Starting Week 5, Mentors will be in lab at 11am.
Dilute new 100 bp ladder in Blue Juice + TE (only a few people) T-shirt Form for VDS shirts
Tuesday, July 1, 2014
HSers - run gels for RE digest
- streak out a plate of PFU Polymerase for growing up
- print PFU polymearase protocol off of Gdocs (GeneMcDonald one)
- print Competent cells protocol and start making some.
FPLC - FtHap: Nikki, Charina, Zain, Andrei, and Luis at 1:00 PM
--- start concentrating down sample ASAP (on last part of either Characterization or Purification protocol?)
--print FPLC protocol
-- then turn on machine
retrieve and clean out old FPLC buffer bottles from Biotech lab
Make Oligo mix for Targets - for those that haven't done it yet (be sure to get the spiel from a Mentor - not from another researcher because there is too much of a 'telephone' gossip effect)
PCR pLIC (2nd practice PCR) - everyone who hasn't done it and has the time
Make FPLC buffers - for those doing YopH tomorrow
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 2, 2014
HSers - Pfu polymerase work, figure out how to make competent cells
- start growing up cultures for overnight expression.
- make glycerol stocks of some of your overnight culture - see GycerolStocks protocol. Store in 80degC in a separate well labelled freezer box.
FPLC - YopH : Chris, Cidia, Andee, Carolyn, Brianna, Hailey at 11:00 AM
Reconcentrate, Snapfreeze in liquid nitrogen, and glycerol store - Nikki, Charina, Zain, Andrei, and Luis
PCRs
RE Digest
5:00 - Naturally Obsessed documentary viewing in Painter.
Thursday, July 3, 2014 Friday, July 4, 2014 - off for 4th of July Saturday, July 5, 2014 Sunday, July 6, 2014
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Protein storage (liguid nitrogen snap freeze to -80degC + 20% glycerol on -20degC)
finish practice PCRs (pLIC PCR)
Make Oligo Mix
Enzyme assay on YopH or FtHap (whichever one you made)
RE Digest
Overlap PCR's (Primary and Secondary)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
Monday, July 7, 2014
MENTOR:
Tally hours from last week and enter into spreadsheet on VDSStaff
Print Travel Forms and fill in date, location etc. - Give to studetns to sign and return.
-- for the lab tour at TACC on Friday (See Summer14 page), Print and have each student sign the release forms (in GDocs ) /MISC/TravelAuthorization
-- enter on Summer 14 page who has gotten theirs turned in so that we know who is missing
RESEARCHERS
Update Wikipages
Update notebooks:
NOTEBOOKS MISSING
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
Info from your Target Page (which means you need a Target page first!)
We will do a notebook check on Wednesday.
HSers:
Pfu Polymerase work
make competent cells and test out
start overnight cultures of Pfu Polymerase colonies in 4ml of LB for Glycerol Stocks tomorrow (see protocol on GDrive)
RE Digest - must be completed before you begin LIC Cloning
Tuesday, July 8, 2014
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
hand out LIC cloning Exercise (due next week)
MENTOR:
check Target pages and note here which need updating (i.e. have missing info)
Wednesday, July 9, 2014
Thursday, July 10, 2014
Friday, July 11, 2014
TACC TOUR
mentors on at 11 if you need to do lab work
1:30 - Meet in Lab to go to the: 2:00 - Bus for the: 2:30 - TACC Machine Room Tour at the Pickle Research Campus
~ 4:30 return back from Tour
Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES
Put a line and 'Week6' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 12, 2014 Sunday, July 13, 2014
Week 7
Monday, July 14, 2014
HSers - test competent cells, test PFU polymerase
ALL - determine what gene is inside pNIC-Bsa4 (i.e. what you get back from DNA Sequencing. You will need to BLAST it and do a little detective work)
Tuesday, July 15, 2014
LIC cloning Exercise due
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 16, 2014 Thursday, July 17, 2014 Friday, July 18, 2014
HSers - enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.
Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES
Put a line and 'Week7' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 19, 2014 Sunday, July 20, 2014
Week 8
Monday, July 21, 2014 HSers - enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.
Tuesday, July 22, 2014
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 23, 2014
Thursday, July 24, 2014
Friday, July 25, 2014
Update your weekly Wikispaces Research page - ALL LINK TO RESEARCH PAGES
Put a line and 'Week8' Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 26, 2014 Sunday, July 27, 2014
Week 9
Monday, July 28, 2014 Tuesday, July 29, 2014 - Last Day of Research for Summer *Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Researcher's Names: VDSers: Andrei, Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
Sidestreamers: Hailey, Zain HSers: Sarah, Minsu, Braxton, Roshni, Caroline W.
Lab Safety: Have you complete your lab safety trainings?
Schedules: please enter your summer schedule here (e.g. classes that you may be taking in the summer or other conflicts with lab work): LINK HERE
Mentors: Want to know when the mentors will be on? - check here Google Calendar
Mentor Conflict sheet
NOTE - see very bottom of page for previous weeks' schedules and things to catch up on that you may have missed.
Mentor Tasks:
make competent cells using Joey's protocol - HSers doing
make PFU polymerase - HSers doing
Set up Mendeley account for VDS. - DONE
Research Presentations Schedule
- see Journal Club ScheduleJournal Club Presentations Schedule
Summer Plasmids
Mentor
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page
THIS WEEK
Dilute new 100 bp ladder in Blue Juice + TE (only a few people)
T-shirt Form for VDS shirts
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Enzyme assay on YopH or FtHap (whichever one you made)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
MENTOR:
Tally hours from last week and enter into spreadsheet on VDSStaff
RESEARCHERS
Update Wikipages - Brianna, Andee, Luis, Martin, Braxton
Update notebooks:
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
Print Journal Club article for you and your friends
Make LB for next week (500ml per person)
Agarose gel checks
Lab Notebook check - should have everything up to date.
-- sleep all day
-- watch TV all day
Dr. B NOTES:
Middle Schoolers visit lab
Cool Stuff We May Not Get To:
Library generation and ligand prep for virtual
Homology modelling
Screening with ICM
- pharmacophore models
DSF (Differential Scanning Fluorimetry) assaysqPCR
Crystallization trials
Staff Stuff:
Label new reagents and supplies
Dilute new 100 bp ladder in Blue Juice + TE
Target Discovery choices --> order primer sets
ToDo List:
Lab Notebook Checks
Protocol cost analysis (Transformation, cloning)
Walk through |protein expression (use current mentor's enzymes)
Wednesday, July 30, 2014Thursday, July 31, 2014
Friday, August 1, 2014
Mentors
Edit SignInSheetCLASS_VDSLabSummer14.xlsx and print several (and hand write date on there)Update Autoclave and Big Centrifuge Protocols and put in binder. Attach Big Centrifuge protocol to Big Centrifuge.
Print 'Sign-Off' sheets for the Biq Equipment usage (See One, Do One, Teach One) -- GDocs/Misc/
--- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Blue.docx - DONE
--- SignOffSheet_SiteSpecific_Centrifuge_Autoclave_etc_Pink.docx - DONE
make Research Pages Summer (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student - DONE Melissa
make Journal Club page for Summer 2014 (see previous journal club for 2013 summer and modify) - DONE Dr. B
Week 1
Post your [[#|class schedule]] to GDOcs - Summer14 - ?Create your own folder in Google Docs under the folder: /StudentFolders
Thursday, June 5
First meeting 3:30 PM - PAI 2.14 (the wet lab)
-- then we will walk over to GEA 100
Lab Safety training
- New guys - walk through with Dr. B
http://vdsstream.wikispaces.com/Required+Lab+Safety
Those that don't have to do Safety Training Walk Through with Dr. B
Pick up primers in MBB with mentors
Dilute some primers
Friday, June 6
1:00 PM start time.......meet in PAI 2.14 to start
Pick up primers at MBB (as a group) - if not already done.
Target Discovery in computer lab WEL 2.128
Saturday, June 7 - watch TV
Sunday, June 8- watch TV
Week 2
Monday, June 9
@ 1pm - Computer lab - Target Disco con't.....
later in afternoon:
Tuesday, June 10
Create your own folder in Google Docs under the folder: /StudentFolders
Make LB (definitely Zain + partner and Hailey + partner) and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans)
LB = 4 x 500 ml amounts
LB plates (20ml per plates) --> make 10 AMP plates (divide into 2 groups) + 36 KAN plates (divide into 3 groups)
to Autoclave
while autoclave go to Nanodrop & submit to DNA sequencing.
Determine concentration of a plasmid (even if it already has it written on the tube!)
(- you pick: pGBR22 or pGFP or pmCherry)
'Learn how to submit to DNA sequencing' (starring Grace et al.) - wet lab
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
Lab Group Meeting @ 5:30 - 6:30 pm
GEA 4031st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496.
Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Wednesday, June 11
Those that don't have to do Safety Training Walk Through with Dr. B
SIgn up for a DNA sequenging [[#|account]] on DNA Lims.
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
Lab clean up
- surfaces, fridges, old plates, old reagents, glassware
re-hang PDB Drug Poster
hang 2014 VDS Stream poster
Organize powdered chemicals
Clean Stir bars
Fill & label spray bottles
Write items needed on whiteboard
Prep collirollers
clean glassware (from Kaarthik)
SHOPPING! ---
go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring several styrofoam containters)
Get stuff from -80degC in Biotech and Robertus Labs (competent cells, protein, etc)
-- store in our -80degC in racks
Proper freezer box label orientation
visit storerooms (walking by ICMB storeroom, then to biotech lab),
purchase the following items (see purchasing spreadsheet in GDocs /Misc/Purchasing) - PRINT IT OUT for 3 teams
- sharpies, spray bottles
- Taq DNA polymerase, 100bp and 1kb ladders
- Mini prep kit, midi prep kit, PCR cleanup kit, IPTG, DTT, TCEP
Enter purchase information in spreadsheet
Place receipt in Dr. B's 'receipt' cubby
prep new kits (midi, mini, PCR cleanup kits)
Analyze DNA Sequence Exercise as a group - ?
Thursday, June 12
Analyze DNA Sequence Exercise as a group -NO
Those that don't have to do Safety Training Walk Through with Dr. B
Choose a Plasmid to work with on these next 2 exercises(pGBR22 or pGFP or pmCherry or pNIC-Bsa4 or pUC19)
Several people: Transform a plasmid for Midi-prep
Some transform expression plasmids (BL21(DE3)) - IF DOING ONE OF THESE _ ALTER THE PROTOCOL TO not USE DH5alphas
In DH5alpha cells for Plasmid Preps:
w/ Amp plates:pGBR22 - Andrei
pGFP - Andee
pmCherry - Briana
w/ Kan plates:
pNIC-Bsa4 - Carolyn, Hailey
pNIC-Bsa4 - Charina, Zain
In BL21(DE3) cells for Protein Expression:
w/ Kan platesFtHap - Chris T., Nikki
YopH - Cidia, Luis
VDSers: Andrei, Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
Sidestreamers: Hailey, Zain
Input information about which culture of plasmid you have (or will) grow up.
http://vdsstream.wikispaces.com/Summer+Plasmids
Grow up colonies of PFU polymerase for eventual midi-prepping. - Melissa
- start 2x 5ml LB overnight culture of Pfu colonies in Kanamycin (use exiisting plate)
- start 2x 5ml of glycerol stocks overnight culture in Kan
- spread 2 x glycerol stocks onto Kan plates.
-- let me know if they grow.
--- then later date proceed to large scale culture
Friday, June 13
check plates - image and upload results to Wikispaces Resarch page and to your Google Docs folder, paste into your lab notebook
- store plates by wrapping in parafilm (just the perimeter) and storing upside down in 4degC in blue racks
Input information about which culture of plasmid you have (or will) grow up.
http://vdsstream.wikispaces.com/Summer+Plasmids
check DNA sequenging results - put on Wiki and in notebook
Clean out fridge by the front of the lab (has a bunch of old LB)
Biohazard Waste Boxing Demonstration
Make more LB+Kan plates, make more LB media for next weeks expressions
Mentor
- make notes about Pfu polymerase in the MentorLabLog - in GDrive
- check Pfu polymerase colony growth from yesterday (from melissa and Grace)
-- if it grew - spread a little bit out on a new Kan plate.
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Summer14 page
Target Discovery selections
Protocol Primer Design OverlapAssembly
Order Overlap Primers for class
On Your Targets Page:
Add Link to DNA Works output text fileAdd substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
Saturday, June 14
Sunday, June 15
WEEK3
Monday, June 16, 2014
Wikispaces:
Update Wikispaces Page: Andee, Andrei, Carolyn, Zain
Just add DNA sequencing result to Wikispaces: Brianna, Charina, Chris, Cidia,Hailey
Completed Wikispaces: Luis, Nicole
Mentor - print new VDS SIgn IN sheets, write dates on them and put in binder (it is in the Google Docs for VDSclass/Scheduling)
Dr. B out 1-3pm, 4-5 pm
Make more LB+Kan plates (10), LB+Kan+Sucrose (20), LB+Amp (10), make more LB media for expressions (2 liters worth, best if they are in separate Erlenmeyer flasks that they will be doing the expessions in)
--e.g. for a 80 ml expression - put it ina 500ml flask
--.e.g for a160 ml expression - put it in a 1000 ml Erlenmeyer flask
-- rule of thumb is that volume of container is 4-5 times bigger than volume of media.
While the autoclave is running, Make some 20% sucrose.
Fill water bath shakers with water and get to temp
[[#|Install]] flask clamps.
Someone do a single transformation of FtHap into BL21(DE3) - just one plate - not the 3 plate thing.
Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware
Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)
Transformation Efficiency calculations.
Mentor - grow up a colony of PFU Polymerase from DR. McDonald overnight.
Mentor - make Research Pages Summer for the new High School students (use http://vdsstream.wikispaces.com/Research+Pages+2013 as a guide) - for each student -
Grow up DH5alpha cells for Plasmid Preps:
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later.-- for each plasmid in DH5alpha, see the MidiPrep protocol
HIGH COPY PLASMIDS:
w/ Amp in 2x80 ml of LB: (80ml is one 'culture's worth. The other 80 ml is a backup)
pGBR22 - Andrei
pGFP - Andee
pmCherry - Briana
LOW COPY PLASMIDS:
w/ Kan in 1x160ml of LB: (160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator)
pNIC-Bsa4 - Carolyn, Hailey, Chris T and Nikki
pNIC-Bsa4 - Charina, Zain, Cidia, Luis
NOTE: the Kan or Amp is not what makes them high or low copy. It is a function of the plasmid. You get more copies of DNA made from a high copy plasmid.
Follow this protocol for the following plasmids: pGBR22, pGFP, pmCherry
ProtocolTransformationforPlasmidPrepVDS.doc
Follow this protocol for the following plasmids: pNic-Bsa4
ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v4
ToDo: next day (Tuesday) spin down your samples. We need to do this in the mid-morning. So, I would like one person to come in around 10:30 and move everyone's Erlenmeyer flasks to the 4degC fridge to 'stop' their growth until the rest of us can get there at 1:00 pm.
5:00-5:30 - Chris T and Carolyn T and Dr. B meet to discuss paper and slides.
Tuesday, June 17, 2014
10:30 - one unlucky person gets to come in and move the flasks to the 4degC fridge. - Nicole W. (mentor)
1:00 PM - spin down your cultures from yesterday. [[#|Store]] pellets in -20degC.
Charina - check FtHap plates
Make some more LB (3 liters)
Make some 20% sucrose.
Clean out fridge by the front of the lab (has a bunch of old LB), wash all this glassware
Biohazard Waste Boxing Demonstration (as in putting waste in a box....not hitting each other. That's not nice)
High Schoolers 1st day
- get setup on GDrive, Wikispaces, etc
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
- PyMol 1 lab
Eventually, someone transform FtHap into BL21(DE3) & DH5alphas
- and transform YopH into DH5alphas
Make 3L LB - Cidia, Luis, Charina
Make 20% Sucrose - Zain, Nikki
My First PCR - Cidia, Luis, Charina, Zain, and Nikki
MidiPrep-
pGBR22 - Andrei and Carolyn
pFGP - Andee, Hailey, Briana
Overnight Cultures for [[#|Protein Expression]]:
YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris
FtHap - Luis & Andrei, Charina & Nikki
Dilute some primers (go in this order until we run out of new primers to dilute) -
Andrei, Hailey, Zain
HSers: Sarah, Minsu, Braxton, Roshni, Caroline W.
Andee, Briana, Carolyn T., Charina, Chris T., Cidia, Luis, Nikki
Lab Group Meeting @ 5:30 - 6:30 pm
GEA 403Reminder to read the Journal Article and bring it with you to meeting
Wednesday, June 18, 2014
Protein Expression - all day - this means that we have to start in the morning (10:00)
HSers - Buffers & Solutions lab
Make IPTG - sterile filter
---- 1 M IPTG in nanopure
Make Lysis buffer (see purification protocol)
submit Midiprep plasmids to DNA sequencing (for those that did Midiprep)
[[#|start]] agarose gels of 1st PCR ?
Luis & Cydia & Nikki
-- start an overnight culture of pNIC-Bsa4 in DH5alpha for making more DNA plasmid for MidiPrep
----2 x 160ml of LB + Kan
-- steal from the plates of: Carolyn, Hailey, Charina, or Zain
-- spin down tomorrow
Thursday, June 19, 2014
HSers - Nanodrop and submit to DNA sequencing pGBR22
Luis, Cydia, Nikki - spin down overnight cultures of DH5alphas
Protein Expression Groups:
YopH - Zain & Cidia, Carolyn & Andee, Hailey & Brianna & Chris
FtHap - Luis & Andrei, Charina & Nikki
Sonication - and store in -20degC
-- These guys start first:
MidiPrep (for those that haven't done it yet) - Zain, Cidia, Chris, Luis, Charina, Nikki
-Use this Kit Protocol for each one.
-ProtocolMidiPrepKit_HiSpeed_VDS_v3.doc
Agarose gels for those that have done PCR.
My first PCR
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Friday, June 20, 2014
HSers - dilute a primer from lyophilized powder
- transformation of pGBr22
Submit samples to DNA Sequencing (group that did Midi-prep yesterday)
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Nickel purify samples from sonication. Collect samples for characterization gel. Store main elution samples in 4degC for next week
start agarose gels of 1st PCR
Restriction Enzyme digest
My First PCR - for those that haven't done it yet
Mentor - grow up overnight culture of pBGR22 in DH5alpha for midi-prep
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
LINK TO RESEARCH PAGES
Put a line and 'Week3'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder
Saturday, June 21, 2014
Sunday, June 22, 2014
Wikispaces updates: Andrei, Charina, Luis, Nikki, Zain
Week 4
PCR pLICSafety training check.
distribute collirollers to tubes (sterily)
Mentor - check lab notebooks to see if up to date.
Monday, June 23, 2014
re-do 1st PCR if failed
- if it works, proceed to PCR pLIC
Analyze DNA Sequence as group
HSers - make more LB,
grow up pGBR22 colonies overnight in 2x80ml of LB each
Print out: Journal article for next week that is posted on Journal Club page and in the GDrive folder
Tuesday, June 24, 2014
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Nickel Purification, Characterization,
practice PCRs
Midi-prep pGBR22 (high schoolers)
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, June 25, 2014
HSers: make LB, make plates, submit DNA to sequencing that you made yesterday
Expression and Spin down for those re-doing protein expression
work on PCRs
Protein Gel for - Andrei, Luis, Andee, Carolyn (maybe do FPLC too?)
Thursday, June 26, 2014
Take ownership of the Target Page for your new target on Wikispaces (update, revise or create page)
http://vdsstream.wikispaces.com/Targets
Lab Tour - there is a lab tour today by visitors - so it is doubly important to wear proper clothing in lab (long pants and close toed shoes)
Purification & Protein gels for people who expressed protein yesterday
FPLC, storage - Andrei, Luis, Andee, Carolyn
Friday, June 27, 2014
11:45 - meet in lab before walking over to POB for the:
12:00 1:00 - TACC VIsLab Tour
https://www.tacc.utexas.edu/resources/visualization
T-shirt Form for VDS shirts
Make Oligo mix for Targets
PCR pLIC (2nd practice PCR)
Design Tail Primers for targets, order tail primers
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
LINK TO RESEARCH PAGES
Put a line and 'Week4'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, June 28, 2014
Sunday, June 29, 2014
WEEK 5
Monday, June 30, 2014
Wikispaces to be updated: Andee, Andrei, Carolyn, Sarah, Martin, Braxton, Caroline, Roshni
Figure out FPLC schedule - who has YopH, vs FtHap. Who can do Wed 11am.
PLASMID INFO
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
PROTEIN INFO
Enter your protein yields into: Protein Spectrophotometer Calc
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodC1mRVpNLVlDOUE4NlNxdldqNEZwRmc&usp=sharing
Design Tail Primers for targets, order tail primers - in Computer Lab
Make Oligo mix for Targets
PCR pLIC (2nd practice PCR)
Make FPLC buffers
print journal club article (and read) for tomorrow - it's a long one!
High schoolers do RE Digest
Week 5
Starting Week 5, Mentors will be in lab at 11am.Dilute new 100 bp ladder in Blue Juice + TE (only a few people)
T-shirt Form for VDS shirts
Tuesday, July 1, 2014
HSers - run gels for RE digest
- streak out a plate of PFU Polymerase for growing up
- print PFU polymearase protocol off of Gdocs (GeneMcDonald one)
- print Competent cells protocol and start making some.
FPLC - FtHap: Nikki, Charina, Zain, Andrei, and Luis at 1:00 PM
--- start concentrating down sample ASAP (on last part of either Characterization or Purification protocol?)
--print FPLC protocol
-- then turn on machine
retrieve and clean out old FPLC buffer bottles from Biotech lab
Make Oligo mix for Targets - for those that haven't done it yet (be sure to get the spiel from a Mentor - not from another researcher because there is too much of a 'telephone' gossip effect)
PCR pLIC (2nd practice PCR) - everyone who hasn't done it and has the time
Make FPLC buffers - for those doing YopH tomorrow
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 2, 2014
HSers - Pfu polymerase work, figure out how to make competent cells
- start growing up cultures for overnight expression.
- make glycerol stocks of some of your overnight culture - see GycerolStocks protocol. Store in 80degC in a separate well labelled freezer box.
FPLC - YopH : Chris, Cidia, Andee, Carolyn, Brianna, Hailey at 11:00 AM
Reconcentrate, Snapfreeze in liquid nitrogen, and glycerol store - Nikki, Charina, Zain, Andrei, and Luis
PCRs
RE Digest
5:00 - Naturally Obsessed documentary viewing in Painter.
Thursday, July 3, 2014
Friday, July 4, 2014 - off for 4th of July
Saturday, July 5, 2014
Sunday, July 6, 2014
Week 6
Dilute new 100 bp ladder in Blue Juice + TE (only a few people)
T-shirt Form for VDS shirts
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Protein storage (liguid nitrogen snap freeze to -80degC + 20% glycerol on -20degC)
finish practice PCRs (pLIC PCR)
Make Oligo Mix
Enzyme assay on YopH or FtHap (whichever one you made)
RE Digest
Overlap PCR's (Primary and Secondary)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
Monday, July 7, 2014
MENTOR:
Tally hours from last week and enter into spreadsheet on VDSStaff
Print Travel Forms and fill in date, location etc. - Give to studetns to sign and return.
-- for the lab tour at TACC on Friday (See Summer14 page), Print and have each student sign the release forms (in GDocs ) /MISC/TravelAuthorization
-- enter on Summer 14 page who has gotten theirs turned in so that we know who is missing
RESEARCHERS
Update Wikipages
Update notebooks:
NOTEBOOKS MISSING
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
We will do a notebook check on Wednesday.
HSers:
Pfu Polymerase work
make competent cells and test out
start overnight cultures of Pfu Polymerase colonies in 4ml of LB for Glycerol Stocks tomorrow (see protocol on GDrive)
RE Digest - must be completed before you begin LIC Cloning
Tuesday, July 8, 2014
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
hand out LIC cloning Exercise (due next week)
MENTOR:
check Target pages and note here which need updating (i.e. have missing info)
Wednesday, July 9, 2014
Thursday, July 10, 2014
Friday, July 11, 2014
TACC TOUR
mentors on at 11 if you need to do lab work
1:30 - Meet in Lab to go to the:
2:00 - Bus for the:
2:30 - TACC Machine Room Tour at the Pickle Research Campus
~ 4:30 return back from Tour
Update your weekly Wikispaces Research page - ALL
LINK TO RESEARCH PAGES
Put a line and 'Week6'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 12, 2014
Sunday, July 13, 2014
Week 7
Monday, July 14, 2014
HSers - test competent cells, test PFU polymerase
ALL - determine what gene is inside pNIC-Bsa4 (i.e. what you get back from DNA Sequencing. You will need to BLAST it and do a little detective work)
Tuesday, July 15, 2014
LIC cloning Exercise due
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 16, 2014
Thursday, July 17, 2014
Friday, July 18, 2014
HSers - enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.
Update your weekly Wikispaces Research page - ALL
LINK TO RESEARCH PAGES
Put a line and 'Week7'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 19, 2014
Sunday, July 20, 2014
Week 8
Monday, July 21, 2014HSers - enter all VDS citations for Poster and Oral presentations into Mendeley and Endnote Web Online.
Tuesday, July 22, 2014
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting
Wednesday, July 23, 2014
Thursday, July 24, 2014
Friday, July 25, 2014
Update your weekly Wikispaces Research page - ALL
LINK TO RESEARCH PAGES
Put a line and 'Week8'
Below that add your 'result' image for the week with brief commentary
This page will run in reverse chronological order - i.e. Newest stuff on top
Saturday, July 26, 2014
Sunday, July 27, 2014
Week 9
Monday, July 28, 2014Tuesday, July 29, 2014 - Last Day of Research for Summer
*Lab Group Meeting @ 5:30 - 6:30 pm in GEA 403
Reminder to read the Journal Article and bring it with you to meeting